If I understood well, you need a jig to enter RCM ? So I assume you don’t have AutoRCM installed, wich means, after AIO updater reboot to a specific payload to launch again AMS after update, it won’t work, as your are not in RCM mode. That’s how I see the issue, but I might be wrong, maybe @Homlet will give the right answer.
Still regardless he still got the fatal error when he try to boot into Atmosphere, assumedly from what it been stated the AIO updater boot into a payload to do it update for Atmosphere, the problem is probably it mess up a file something causing the fatal error, I had mine on AutoRCM and still error also, so problem is how the updater overwrite and replace the file.